Genome Organisation, Structure & Replication

Intended Learning Outcomes (ILOs)

  • At the end of this lecture, students will be able to:

    • Describe the structure of nucleic acids

    • Compare and contrast the main functions and features of DNA and RNA

    • Explain the double-helix structure of DNA

    • Outline the main steps of eukaryotic DNA replication

    • Discuss the importance of accurate DNA replication

Key Definitions

  • Genome: A complete set of genetic instructions for any organism, either in RNA or DNA. It is copied during replication.

  • RNA: Acts as a bridge between genes and proteins, typically through two processes:

    • Transcription: The synthesis of RNA using DNA information, producing mRNA for protein coding genes.

    • Translation: The synthesis of a polypeptide using mRNA information, which occurs at the ribosomes.

  • Ribosomes: The cellular structures where translation occurs.

  • Central dogma: Information cannot be transferred from protein to protein , nor can it be transferred from protein back to nucleic acids; it flows in one direction: DNA to RNA to protein only

  • ONLY one EXCEPTION OF RNA TO DNA

Characteristics of Genetic Material

  • Must contain complex information.

  • Needs to replicate faithfully (copy itself).

  • Must encode all phenotypes of the organism.

  • Should have the capacity to vary (genetic variability).

Common Themes in Living Organisms

  • Physical separation defines self and non-self, allowing the organism to interact with its environment.

  • Stable yet flexible storage of the genome.

  • Reliable replication and transmission of genetic information for offspring and tissue generation.

  • A source of energy is required for growth and reproduction, e.g. sunlight for plants and food for humans.

Genome Size Comparison Among Species

shows how genome doesn’t correlate to complextity

Species

Genome Size

Common Name

T2 phage

170,000 bp

Virus

Escherichia coli

4.6 million bp

Bacteria

Drosophila melanogaster

130 million bp

Fruit Fly

Homo sapiens

3.2 billion bp

Human

Paris japonica

150 billion bp

Canopy Plant

Historical Timeline: Discovery of DNA Structure

  • 1833: Brown describes the nucleus of the cell.

  • 1869: Miescher discovers nuclein (DNA) in white blood cell nuclei.

  • 1884: Isolation of histones from the nucleus.

  • 1900: Mendel's work on genetic inheritance is re-established.

  • 1910: Levene proposes the tetranucleotide theory.

  • 1928: Griffith demonstrates the “transformation principle”.

  • 1944: Avery, MacLeod, and McCarty show DNA is the “transforming factor”.

  • 1947: Ashbury begins X-ray diffraction studies of DNA.

  • 1952: Hershey and Chase prove DNA is the genetic material in bacteriophage.

  • 1953: Watson and Crick devise the double-helix structure of DNA after WL Franklin and M Wilkins produce X-ray images.

  • 1962: Watson, Crick, and Wilkins awarded the Nobel Prize in Physiology or Medicine.

Anatomy of a Cell: Components and Functions

  • Nucleus: Contains genetic material in the form of chromatin.

  • Dna has also been found in mitochondria and chloroplast due to endosymbiosis

  • Nucleolus: Primary function is ribosome synthesis and assembly.

  • Ribosomes: Sites of protein synthesis, transported from the nucleolus to the cytoplasm.

  • Endoplasmic Reticulum (smooth and rough): Functions in protein synthesis and lipid metabolism.

  • Golgi Apparatus: Modifies and packages proteins for secretion.

  • Mitochondria: Powerhouse of the cell, involved in energy production.

Structure of Nucleic Acids

  • Nucleotides: Monomers of nucleic acids, containing a nitrogenous base, a sugar (ribose in RNA, deoxyribose in DNA), and a phosphate group.

  • Components include:

    • Nitrogen base: Adenine (A), Guanine (G), Cytosine (C), Thymine (T), and Uracil (U) (the last one only in RNA).

  • Chemical structure: DNA is a polymer of nucleotides linked by phosphodiester bonds, forming a sugar-phosphate backbone.

DNA Structure

  • DNA is organized into double-helical structure:

    • The B-form DNA is characterized by two polynucleotide chains that run antiparallel.

    • Diameter: 20 Å.

    • Complete turn every 34 Å, with 10 base pairs per turn.

  • Stability: Hydrogen bonds and base stacking contribute to the double helix's stability.

  • Base Pairing Rules: A pairs with T, C pairs with G (Chargaff’s rules).

  • differences of RNA and DNA: sugars, bases, double stranded vs single stranded

  • Purines: Adenine and Guanine. has 2 carbon rings

  • pyridines: cytosine, uracil and thymine. Only has 1 carbon rings

  • A and T only hand 2 hydrogen bonds while C and T has 3.

  • Angstrom: 10th of a nanometre

  • Histones: type of protein that packs DNA in highly compact shape: chromatin.

  • Nucleosomes: structural units of chromatin formed by a segment of DNA wound around a core of histone proteins, playing a crucial role in the organization of DNA within the nucleus.

  • Two types of chromatin:

  • Euchromatin: Less condensed form of chromatin that is often transcriptionally active, allowing genes to be expressed.

  • Heterochromatin: Densely packed form of chromatin that is generally transcriptionally inactive, serving structural and regulatory functions.

DNA Replication

Chargaff’s rule: no.1 of A=T and C=G

  • Semiconservative Process: Each strand of DNA acts as a template for the synthesis of a new complementary strand. discovered by Meselson and Stahl.

  • Process Initiation:

    • Starts at multiple origins of replication. originally started by initiator proteins for access of DNA Helicase.

    • Replication forks move bidirectionally.

  • Elongation:.

    • Occurs from 5’ to 3’ direction.

    • Primase synthesizes RNA primers for DNA polymerase to build upon.

    • Leading strand synthesized continuously ( the side helicase is breaking bonds), lagging strand in fragments the strand has to go right too left (still 5’ to 3’ due to antiparallel and causes smaller DNA fragments and its discontinuous called Okazaki fragments) ).

  • Enzymatic Activities:

  • DNA Helicase breaks hydrogen bonds

    • DNA polymerases have proofreading and exonuclease activity to ensure accuracy.

    • DNA ligase- join Okazaki fragments

  • Telomeres: Special sequences at the ends of eukaryotic DNA that help postpone the erosion of essential genetic material.

DNA Repair Mechanisms

telomeres are long repetitive sequences that protect chromosome ends and maintain genomic stability during DNA replication. However it cannot prevent shortening of DNA molecules but do postpone erosion of limitations of DNA polymerase (always creating a short DNA fragment on the lagging strand)

  • Defined as inherited alterations in the DNA sequence that can arise from replication errors or damage from external factors.

  • Mechanisms exist to detect and repair these errors to maintain genomic integrity.

Recent Advances in DNA Technology

  • PCR Development: By Kary Mullis in 1983, Nobel Prize awarded in 1993.

  • CRISPR-Cas9 Genome Editing: Awarded the Nobel Prize in 2020.